Mexico City; and La Paz, Bolivia — When Evo Morales was elected Bolivia's first indigenous president in 2005, José Ortiz, a national indigenous leader, was hopeful.

But today Mr. Ortiz stands in Plaza San Francisco in Bolivia's administrative capital of La Paz protesting against the man who was once his key ally. Marchers carry signs calling Mr. Morales a liar during a nationwide strike after police quashed a deadly protest against a road through rain forest that the government vowed to build, despite indigenous protests.

"At the beginning it was different; we worked together. The government even comes from humble beginnings. It identified itself as an indigenous government." Now, he says, "we've lost confidence."

Morales's election, followed by inaugurations across the region of presidents promising more social inclusion, had spurred hopes that new leaders would stand up for the interests of native peoples. But many groups are increasingly butting heads with the governments they elected and demanding greater participation in decisions that affect their ancestral lands, especially as it relates to massive energy and infrastructure projects these fast-growing nations see as key to their development.

Rifts in the Andean region

A case in point is Bolivia, where police confronted those protesting a proposed new road, heavily financed by Brazil, that was to cut through The National Park and Indigenous Territory Isiboro-Secure (TIPNIS). The indigenous living in the lowland jungle say their rights to be previously consulted, enshrined in the new 2009 Constitution, have been violated and fear the road will open the park to oil and gas exploration and an influx of coca growers, among other concerns.

The movement has come to a head, with two ministers resigning – one in solidarity, another under pressure – over allegations that the government ordered police to crush the movement. Morales halted the project. But he said he might put its future to a broad referendum, which the marchers oppose.

More than 60 percent of Bolivia's population identifies itself as ethnically indigenous, and while they are hardly monolithic – some support Morales's highway – this protest has cost Morales support among many of his former allies. In the scandal's wake, he called protesters his "indigenous brothers," but at an earlier point labeled them lackeys of the United States.

"When he was campaigning he said, 'If you all support me and vote for me I will be the president of the disadvantaged.' So we, the indigenous peoples, decided to support for him,” says Cecilia Moyobire, president of Moxeno Trinitario group of the southern part of the TIPNIS. “We trusted in him and voted because with other governments we were always forgotten, discriminated against, crushed, and massacred.”

The indigenous have also lost a key ally in Ecuador. Groups largely supported the rise of President Rafael Correa and the passage of his 2008 Constitution recognizing a "plurinational" state, but battles have erupted as the indigenous charge that Mr. Correa cares more about resource development than land rights. The president, for his part, has done little to seek compromise, instead putting indigenous leaders and their supporters under investigation for charges such as sabotage. To some analysts, the rifts in the Andean region show the dilemmas posed by fulfilling campaign promises while running modern economies.

"Correa and Morales came to power reclaiming rights against foreign investment, but they still need it," says Christopher Sabatini, editor in chief of the policy journal Americas Quarterly in New York.

They also can't please every faction under the umbrella of a national indigenous community, a community that does not share one platform but has many competing demands, claims, and grievances. And Mr. Sabatini say indigenous groups need new agendas that not only address age-old narratives of land rights but begin to tackle their lack of access to education, health, and other services.

Consultation may encourage claims

Many Latin American nations have signed the International Labor Org­an­iza­tion Convention that asserts native rights to land and prior consultation, says Max­well Cameron, an expert in Latin Amer­ican democratization at the Uni­versity of British Columbia. But in reality, countries differ on how those concepts are put into practice. In Guatemala, for example, despite hundreds of consultations, indigenous claims have been ignored, he says.

Some of the most conflictive protests by indigenous against development and resource extraction in particular have occurred in Peru. In August, the National Congress approved a law that requires companies to consult with communities before commencing projects on their territories.

But when indigenous concerns are taken into account, that could increase – not decrease – conflict. "A mechanism for consultation actually empowers people to make claims," Mr. Cameron says. "It doesn't mean that conflicts go away."

And at the root of the issue in Bolivia is vague terminology over what “consultation” means, how it is conducted, and whether indigenous communities have the last word on whether a project proceeds or not. These are some of the questions that will be grappled with in Bolivia and beyond as the indigenous navigate new powers.

"Historically the Constitution [in Bolivia] remains a highly important step for the rights of indigenous peoples," says Robert Albro, an expert on social and indigenous movements in Latin America at American University. "That is unequivocal," he says. "But it does not make it un-problematically good."